Gene network analysis is a powerful tool to identify and prioritize candidate genes, especially from data sets where experimental design renders other approaches, such as differential expression analysis, limiting or infeasible. Numerous gene network inference algorithms have been published and are commonly individually applied in transcriptomics studies. It has, however, been shown that every algorithm is biased towards identifying specific types of gene interaction and that an ensemble of inference methods can reconstruct more accurate networks. This approach has been hindered by lack of an implementation to run and combine such combinations of inference algorithms. Here, we present Seidr: a toolkit to perform multiple gene network inferences and combine their results into a unified meta-network. Availability and implementation:Seidr code is open-source, available from GitHub and also compiled in docker and singularity containers. It is implemented in C++ for fast computation and supports massive parallelisation through MPI. Documentation, tutorials and exemplary use are available from https://seidr.readthedocs.io.

Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed extensive reversible plasticity for physiological measures indicative of drought response mechanisms, including changes in stomatal conductance (gs), shoot water potential and ABA (abscisic acid). In both tissues the most commonly observed expression profiles in response to drought were highly correlated with ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific downregulation of growth. Comparison between previously characterized A. thaliana drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the bZIP AREB/ABF (ABA Response Element Binding/ABRE Binding Factors) ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and below-ground tissues and provide a comprehensive framework to advance understanding of the drought response of P. abies. The results demonstrate that short term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.

Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.